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Graphormer (DeepProtein benchmark)

Configuration of Graphormer: graph model; default DeepProtein configuration.

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Evaluations and results

8 evaluations · 8 results. Different protocols are not a single leaderboard.

Sorted by MAE (mean absolute error) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	MAE (mean absolute error)	Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)	AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.287 ± 0.007 (best in column)	Not reported	Not reported	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	1.201 ± 0.032	Not reported	Not reported	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	0.067±0.046 (best in column)	Not reported	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	0.058±0.015	Not reported	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	Not reported	Not reported	OOM%
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	OOM%	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	OOM	Not reported	Not reported	Not reported
Graphormer (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	OOM	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.287 ± 0.007 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein beta-lactamase (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-beta-lactamase-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'β-lactamase', column 'MAE ↓'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.067±0.046 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.046 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein beta-lactamase (PEER) (ρ ↑) lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	1.201 ± 0.032 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.032 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Fluorescence (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-fluorescence-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Fluorescence', column 'MAE ↓'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.058±0.015 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Fluorescence (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-fluorescence-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Fluorescence', column 'ρ ↑'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	OOM% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Solubility (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-solubility-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	OOM% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Solubility (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-solubility-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Solubility', column 'PR-AUC ↑'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	OOM MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Stability (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-stability-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Stability', column 'MAE ↓'
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	OOM Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein Stability (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-stability-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'Stability', column 'ρ ↑'

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DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)

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Technical metadata and extraction receipts

Stable ID: lit-protein-20261011-deepprotein-config-graphormer

areas: protein-function
contexts: research
method types: specialist
reported name: Graphormer
reported configuration: graph model; default DeepProtein configuration (Table 9)
foundation model eligible: false
source locator: Tables 2 to 8, row 'Graphormer'; Table 9 for the default configuration
missing metadata: version: reason: unreported; note: The tables name the model without a release version
provenance note: Graphormer as trained and evaluated in the DeepProtein benchmark (graph model).

Related records

configuration of: Graphormer
system: Graphormer on DeepProtein beta-lactamase (PEER) (MAE ↓)
system: Graphormer on DeepProtein beta-lactamase (PEER) (ρ ↑)
system: Graphormer on DeepProtein Fluorescence (TAPE) (MAE ↓)
system: Graphormer on DeepProtein Fluorescence (TAPE) (ρ ↑)
system: Graphormer on DeepProtein Solubility (PEER) (Averaged F1 ↑)
system: Graphormer on DeepProtein Solubility (PEER) (PR-AUC ↑)
system: Graphormer on DeepProtein Stability (TAPE) (MAE ↓)
system: Graphormer on DeepProtein Stability (TAPE) (ρ ↑)

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